Variant report

Variant	rs6561511
Chromosome Location	chr13:49835110-49835111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10459375	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459376	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11619804	0.80[CHB][hapmap]
rs11843587	0.82[EUR][1000 genomes]
rs12385878	0.84[EUR][1000 genomes]
rs12585196	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1555672	0.91[CEU][hapmap]
rs1924659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924661	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038759	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2147398	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2181905	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2274149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407521	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2407607	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407609	0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3087770	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4444233	0.82[JPT][hapmap]
rs4941637	1.00[CEU][hapmap];0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs4942809	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942811	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942815	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs719614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320595	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320745	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326181	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7326191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328063	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7330892	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7334929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988621	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7999710	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316437	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316439	0.90[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526535	0.86[ASN][1000 genomes]
rs9526537	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526538	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526539	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535173	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535177	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535182	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535185	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535190	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535192	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535194	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535197	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs9535198	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs9535199	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9562873	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568174	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568176	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568179	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568181	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568182	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9591249	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9596077	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596078	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9596079	0.83[EUR][1000 genomes]
rs9596080	0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49823000-49836400	Weak transcription	Colonic Mucosa	Colon
2	chr13:49823000-49837000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:49823000-49838000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:49823000-49838200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr13:49823000-49844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:49823400-49837200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr13:49823400-49837400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr13:49823400-49837600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr13:49823400-49844000	Weak transcription	A549	lung
10	chr13:49823600-49835200	Weak transcription	K562	blood
11	chr13:49823600-49837400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr13:49823600-49843200	Weak transcription	NHEK	skin
13	chr13:49823800-49855400	Weak transcription	Small Intestine	intestine
14	chr13:49826600-49877800	Weak transcription	Psoas Muscle	Psoas
15	chr13:49827600-49837200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr13:49827800-49837000	Strong transcription	Fetal Muscle Trunk	muscle
17	chr13:49827800-49837800	Strong transcription	Fetal Lung	lung
18	chr13:49827800-49839400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr13:49828800-49836600	Strong transcription	Fetal Muscle Leg	muscle
20	chr13:49828800-49837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr13:49829200-49835400	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr13:49829200-49836000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr13:49830400-49835200	Strong transcription	HepG2	liver
24	chr13:49831200-49837600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr13:49831200-49845200	Weak transcription	NH-A	brain
26	chr13:49831600-49837000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr13:49831600-49837000	Strong transcription	Fetal Stomach	stomach
28	chr13:49831800-49836200	Strong transcription	Fetal Brain Female	brain
29	chr13:49832000-49843000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:49832200-49836200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr13:49832400-49837000	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr13:49832600-49836400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr13:49832600-49836400	Strong transcription	Fetal Thymus	thymus
34	chr13:49832600-49836600	Strong transcription	Primary B cells from cord blood	blood
35	chr13:49832800-49835600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr13:49832800-49836600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr13:49832800-49838200	Strong transcription	NHDF-Ad	bronchial
38	chr13:49832800-49838600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr13:49832800-49844800	Strong transcription	Dnd41	blood
40	chr13:49832800-49860600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr13:49832800-49862800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr13:49833000-49835400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr13:49833000-49837200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr13:49833000-49865600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr13:49833200-49836600	Strong transcription	Brain Anterior Caudate	brain
46	chr13:49833200-49852600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr13:49833200-49863800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr13:49833200-49866600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr13:49833400-49836400	Strong transcription	Fetal Intestine Large	intestine
50	chr13:49833400-49836600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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